I see slightly different but still weird behaviour. When selecting the entirety of lines 2 and 3, and run M-x comment-region, I get this:
#+BEGIN_SRC emacs-lisp ;; (defun org-xor (a b) ;; "Exclusive or." ;; ( if a (not b) b)) #+END_SRC Versions: GNU Emacs 29.4 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.43, cairo version 1.18.2) Org mode version 9.6.15 (release_9.6.15 @ /usr/share/emacs/29.4/lisp/org/)